Contacts of the strand formed by residues 112 - 117 (chain A) in PDB entry 2FD6


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with TRP 112 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  TRP*     4.0     8.1    -      +       -      -
     84A  TYR*     3.8    10.1    -      +       -      -
    102A  CYS*     3.1     6.9    -      -       -      -
    103A  ARG      2.8    38.4    +      -       -      +
    104A  ASN*     3.1    22.6    +      -       -      +
    105A  PRO*     3.6    14.1    -      -       +      -
    106A  ASP*     2.7    43.1    +      -       -      -
    108A  ARG*     3.7    14.6    -      -       -      +
    110A  ARG      3.6     6.5    -      -       -      +
    111A  PRO*     1.3    74.4    -      -       -      +
    113A  CYS*     1.3    99.8    +      -       -      +
    114A  TYR*     3.8    33.0    -      +       -      -
    123A  VAL*     3.6    28.9    -      -       +      -
    124A  GLN      3.2    22.4    -      -       -      +
    125A  GLU*     4.3     3.1    -      -       +      -
    126A  CYS*     3.9     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  THR      5.1     1.6    -      -       -      -
     65A  ASP*     5.4     2.2    -      -       -      -
     71A  CYS*     2.0    56.1    -      -       +      -
     72A  LEU      5.7     0.4    -      -       -      +
     74A  TRP*     4.0    15.9    -      -       +      -
    101A  TYR      4.9     0.2    -      -       -      +
    102A  CYS*     4.3     7.9    -      -       -      +
    112A  TRP*     1.3    96.8    -      -       -      +
    114A  TYR*     1.3    61.0    +      -       -      +
    115A  VAL*     3.6    12.6    +      -       -      +
    124A  GLN      3.0    29.6    +      -       -      -
    125A  GLU      5.9     0.2    -      -       -      -
    126A  CYS*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  CYS*     3.5     3.5    -      -       -      -
     72A  LEU*     2.8    38.8    +      -       +      +
     74A  TRP*     3.9    14.1    -      +       -      -
     79A  VAL*     3.6    34.8    -      -       +      -
     82A  GLN*     3.5    30.5    +      -       +      +
     83A  THR*     3.5    13.2    +      -       -      -
     84A  TYR*     3.1    41.8    +      -       -      +
    112A  TRP*     3.8    18.7    -      +       -      -
    113A  CYS*     1.3    72.4    -      -       -      +
    115A  VAL*     1.3    59.9    +      -       -      +
    121A  PRO*     4.8     8.1    -      -       +      -
    122A  LEU      3.8     3.6    -      -       -      -
    123A  VAL*     3.5    33.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ASP*     4.1     9.6    -      -       +      -
     69A  ARG*     3.4    42.8    -      -       +      +
     70A  PRO*     3.8    14.8    -      -       +      +
     71A  CYS*     4.5     0.4    -      -       -      -
     72A  LEU*     4.1     2.9    -      -       -      -
    113A  CYS*     3.8    17.3    -      -       -      -
    114A  TYR*     1.3    80.1    -      -       -      +
    116A  GLN*     1.3    70.4    +      -       -      +
    117A  VAL*     3.5     4.4    +      -       +      +
    122A  LEU*     2.8    33.6    +      -       -      +
    124A  GLN*     3.3    36.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ARG*     4.9     4.5    -      -       -      +
     70A  PRO      4.6     2.4    +      -       -      +
     72A  LEU*     3.8    27.0    -      -       +      +
     78A  THR*     4.2    13.0    +      -       -      +
    115A  VAL*     1.3    79.6    -      -       -      +
    117A  VAL*     1.3    67.4    +      -       -      +
    118A  GLY      3.4    14.9    +      -       -      +
    119A  LEU      3.2    10.0    -      -       -      +
    120A  LYS      3.0    42.3    +      -       -      +
    121A  PRO*     4.0    17.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ARG*     3.8    34.1    -      -       -      +
    115A  VAL*     4.1     8.3    -      -       +      +
    116A  GLN*     1.3    80.4    -      -       -      +
    118A  GLY*     1.3    60.8    +      -       -      +
    119A  LEU      3.0     8.8    +      -       -      -
    120A  LYS*     3.0    25.4    +      -       +      +
    122A  LEU*     4.3    20.6    -      -       +      -
    124A  GLN*     5.3     4.9    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il